ASL-BIDS, the brain imaging data structure extension for arterial spin labeling

Clement, Patricia; Castellaro, Marco; Okell, Thomas W.; Thomas, David L.; Vandemaele, Pieter; Elgayar, Sara; Oliver-Taylor, Aaron; Kirk, Thomas; Woods, Joseph G.; Vos, Sjoerd B.; Kuijer, Joost P.A.; Achten, Eric; Osch, Matthias J.P. van; Appelhoff, Stefan; Blair, Ross; Feingold, Franklin; Gau, Rémi; Markiewicz, Chris; Salo, Taylor; Detre, John A.; Lu, Hanzhang; Alsop, David C.; Chappell, Michael A.; Hernandez‐García, Luis; Petr, Jan; Mutsaerts, Henk‐Jan

doi:10.1038/s41597-022-01615-9

Cited by 24 publications

(26 citation statements)

References 30 publications

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“…The results in Table 2 showed that the volume and CBF values of brain regions such as frontal lobe, temporal lobe, and basal ganglia were lower in ADHD children than in healthy children, suggesting poor development of those brain regions and decreased CBF perfusion in ADHD children. The poor development of frontal lobe, temporal lobe, and basal ganglia in ADHD children may be due to the poor development of brain regions caused by longterm inadequate blood perfusion in these three brain regions, which ultimately leads to the development of clinical symptoms such as hyperactivity in ADHD children (42)(43)(44). The results showed that the gray matter volume and CBF values of brain regions such as frontal lobe, temporal lobe and basal ganglia were lower in ADHD children with ADHD than in healthy children, but only the volume of white matter was lower than in healthy children, and the difference in CBF values was not statistically significant, suggesting that the microstructural changes in the brain of ADHD children are mainly in the gray matter, which is probably because there is more blood flow in the gray matter and less blood flow in the white matter.…”

Section: Discussionmentioning

confidence: 99%

Three-dimensional pseudocontinuous arterial spin labeling perfusion imaging shows cerebral blood flow perfusion decline in attention-deficit/hyperactivity disorder children

Tang

Liu²,

Nie³

et al. 2023

Front. Psychiatry

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PurposeTo investigate the feasibility of three-dimensional pseudocontinuous arterial spin labeling (3D-pcASL) perfusion imaging in the brain of children with Attention-deficit/hyperactivity disorder (ADHD).MethodsA total of 78 ADHD children aged 5–13 years were prospectively selected as the study group, and 89 healthy children matched in age and sex were selected as the control group. All children underwent MRI conventional sequence, 3D-pcASL, and 3D-T1 sequence scans. The brain gray and white matter volume and cerebral blood flow (CBF) perfusion values were obtained by software post-processing, and were compared and analyzed in the two groups to find out their characteristics in the brain of ADHD children.ResultsThe total brain volume and total CBF values were lower in ADHD children than in healthy children (P < 0.05); the gray and white matter volumes in the frontal lobe, temporal lobe, hippocampus, caudate nucleus, putamen, globus pallidus and other brain regions were lower in ADHD children than in healthy children (P < 0.05); the gray matter CBF values in the frontal lobe, temporal lobe, hippocampus, caudate nucleus, putamen, globus pallidus and other brain regions were lower in ADHD children than in healthy children (P < 0.05); the differences between the white matter CBF values of white matter in the said brain regions of ADHD children and healthy children were not statistically significant (P > 0.05); and the CBF values in frontal lobe and caudate nuclei could distinguish ADHD children (AUC > 0.05, P < 0.05).ConclusionThe 3D-pcASL technique showed reduced cerebral perfusion in some brain regions of ADHD children.

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Section: Discussionmentioning

confidence: 99%

Three-dimensional pseudocontinuous arterial spin labeling perfusion imaging shows cerebral blood flow perfusion decline in attention-deficit/hyperactivity disorder children

Tang

Liu²,

Nie³

et al. 2023

Front. Psychiatry

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“…Less than half of the pipelines support imports from the clinically used DICOM format (n = 9). Only three pipelines support ASL‐BIDS, 32 the recently developed ASL extension of the standard for storing image data and acquisition metadata. All pipelines were developed for human brain data, and only a few were reported to be suited also for body imaging in humans (n = 3) and preclinical brain imaging (n = 3).…”

Section: Resultsmentioning

confidence: 99%

“…20 More than 20 different toolboxes have been released for ASL data processing and analysis 16,19,[21][22][23][24][25][26][27][28][29][30][31] from different laboratories that specialize in ASL analysis. The selection of a particular pipeline by a new user can be complicated because of the wide variety of ASL sequences, data formats, 32 and processing methods. 19 Both new and experienced ASL users looking for suitable ASL image processing and quantification software may benefit from a comprehensive and detailed list of ASL image-processing software along with their features to guide their search for a suitable pipeline.…”

Section: Introductionmentioning

confidence: 99%

ISMRM Open Science Initiative for Perfusion Imaging (OSIPI): ASL pipeline inventory

Fan,

Mutsaerts,

Anazodo

et al. 2023

Magnetic Resonance in Med

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PurposeTo create an inventory of image processing pipelines of arterial spin labeling (ASL) and list their main features, and to evaluate the capability, flexibility, and ease of use of publicly available pipelines to guide novice ASL users in selecting their optimal pipeline.MethodsDevelopers self‐assessed their pipelines using a questionnaire developed by the Task Force 1.1 of the ISMRM Open Science Initiative for Perfusion Imaging. Additionally, each publicly available pipeline was evaluated by two independent testers with basic ASL experience using a scoring system created for this purpose.ResultsThe developers of 21 pipelines filled the questionnaire. Most pipelines are free for noncommercial use (n = 18) and work with the standard NIfTI (Neuroimaging Informatics Technology Initiative) data format (n = 15). All pipelines can process standard 3D single postlabeling delay pseudo‐continuous ASL images and primarily differ in their support of advanced sequences and features. The publicly available pipelines (n = 9) were included in the independent testing, all of them being free for noncommercial use. The pipelines, in general, provided a trade‐off between ease of use and flexibility for configuring advanced processing options.ConclusionAlthough most ASL pipelines can process the common ASL data types, only some (namely, ASLPrep, ASLtbx, BASIL/Quantiphyse, ExploreASL, and MRICloud) are well‐documented, publicly available, support multiple ASL types, have a user‐friendly interface, and can provide a useful starting point for ASL processing. The choice of an optimal pipeline should be driven by specific data to be processed and user experience, and can be guided by the information provided in this ASL inventory.

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“…The parameters related to ASL labeling methods are provided in Table 5. In general, the names and definitions of parameters comply with the ASL White Paper, 1 as well as ASL-BIDS 4 ; otherwise, the difference is provided in the description. In general, for timing parameters there is no preference between the use of "ms" and "s." In ASL-BIDS, however, the values in JSON sidecars are entered without specifying the units; therefore, the use of correct units, as specified in the ASL-BIDS definition, should be strictly followed.…”

Section: Parameters In Asl Labeling Methodsmentioning

confidence: 99%

ASL lexicon and reporting recommendations: A consensus report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI)

Suzuki,

Clement,

Dai

et al. 2023

Magnetic Resonance in Med

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The 2015 consensus statement published by the International Society for Magnetic Resonance in Medicine (ISMRM) Perfusion Study Group and the European Cooperation in Science and Technology ( COST) Action ASL in Dementia aimed to encourage the implementation of robust arterial spin labeling (ASL) perfusion MRI for clinical applications and promote consistency across scanner types, sites, and studies. Subsequently, the recommended 3D pseudo‐continuous ASL sequence has been implemented by most major MRI manufacturers. However, ASL remains a rapidly and widely developing field, leading inevitably to further divergence of the technique and its associated terminology, which could cause confusion and hamper research reproducibility.On behalf of the ISMRM Perfusion Study Group, and as part of the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI), the ASL Lexicon Task Force has been working on the development of an ASL Lexicon and Reporting Recommendations for perfusion imaging and analysis, aiming to (1) develop standardized, consensus nomenclature and terminology for the broad range of ASL imaging techniques and parameters, as well as for the physiological constants required for quantitative analysis; and (2) provide a community‐endorsed recommendation of the imaging parameters that we encourage authors to include when describing ASL methods in scientific reports/papers.In this paper, the sequences and parameters in (pseudo‐)continuous ASL, pulsed ASL, velocity‐selective ASL, and multi‐timepoint ASL for brain perfusion imaging are included. However, the content of the lexicon is not intended to be limited to these techniques, and this paper provides the foundation for a growing online inventory that will be extended by the community as further methods and improvements are developed and established.

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ASL-BIDS, the brain imaging data structure extension for arterial spin labeling

Cited by 24 publications

References 30 publications

Three-dimensional pseudocontinuous arterial spin labeling perfusion imaging shows cerebral blood flow perfusion decline in attention-deficit/hyperactivity disorder children

Three-dimensional pseudocontinuous arterial spin labeling perfusion imaging shows cerebral blood flow perfusion decline in attention-deficit/hyperactivity disorder children

ISMRM Open Science Initiative for Perfusion Imaging (OSIPI): ASL pipeline inventory

ASL lexicon and reporting recommendations: A consensus report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI)

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